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LRRprofiler_v0.2_sing_3.6.def
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LRRprofiler_v0.2_sing_3.6.def
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BootStrap: library
From: ubuntu:18.04
%help
This container launches the LRRprofiler pipeline used to annot proteins with Leucine Rich Repeat motifs.
=======================================================================================
usage (help) : singularity run LRRprofiler_v0.1.sif
usage (basic) : singularity run LRRprofiler_v0.1.sif --in_proteome <fasta file> --name <string>
usage (example): singularity run LRRprofiler_v0.1.sif --in_proteome example/Arabidopsis_Thaliana_reviewed_proteom_SwissProt_05-2020.fasta --name ARATH
building container : singularity build LRRprofiler_v0.1.sif LRRprofiler_v0.1_sing_3.6.def
For more details please see the pipeline documentation pages on the LRRprofiler website:
==================================================================================
#https://github.com/cgottin/LRRprofiler
If you use this pipeline please cite:
=====================================
--------------------------------------
MAFFT v7.271
Katoh K., Standley D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4), 772-780. Edgar R.C. (2004).
SMART database
Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
HMMER v3.1b2
S. R. Eddy. (2011) Accelerated profile HMM searches. PLoS Comp. Biol., 7:e1002195
iTAK
Zheng Yet al. (2016) iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant 9:1667-1670.
--------------------------------------
%files
tmhmm2.0c.tar
%post
apt-get -y update
apt-get -y install software-properties-common
add-apt-repository universe
apt-get -y update
apt-get -y install python3-biopython
apt-get -y install gawk
apt-get -y install unzip
apt-get -y install wget
apt-get -y install hmmer
apt-get -y install mafft
apt-get -y install pandoc-data
apt-get -y install pandoc
apt-get -y install bioperl
#apt-get -y install subversion
apt-get -y install git
apt-get -y update
## getting scripts from github
#svn checkout https://github.com/kentnf/iTAK/trunk/
#mv trunk iTAK
git clone https://github.com/kentnf/iTAK.git
chmod -R 777 /iTAK/
git clone --single-branch --branch master https://github.com/cgottin/LRRprofiler.git
chmod 777 /LRRprofiler/src/*
tar -xf /tmhmm2.0c.tar
chmod -R 777 /tmhmm2.0c/
apt-get purge -y --auto-remove wget unzip git #subversion
# running iTAK on test set to set up files
perl /iTAK/iTAK.pl /iTAK/test_seq
apt-get -y install r-base
apt-get -y install r-base-dev
R --slave -e 'install.packages(c("rmarkdown","ggplot2","reshape2"))'
rm -rf /var/lib/apt/lists/*
apt-get clean
%environment
export LC_ALL=C
export LG_SCRIPT="/LRRprofiler/src"
export LG_HMMlib="/LRRprofiler/HMM_lib"
export LG_MAFFT="mafft"
export LG_ITAK="/iTAK/iTAK.pl"
export LG_TMHMM="/tmhmm2.0c/bin/tmhmm"
R_VERSION=3.6.1
export R_VERSION
R_CONFIG_DIR=/etc/R/
export R_CONFIG_DIR
export PATH=$PATH
%runscript
exec bash /LRRprofiler/src/LRRprofiler_global.sh "$@"
%labels
Author Céline Gottin & Vincent Ranwez